[Annoying bump] – I know this might sound like a painfully obvious thing to have to point out, but I really am struggling to find an answer here. Hours of googling have returned nothing. I’d be highly, highly appreciative if one of you could help me.

Easiest way is to save the master patch without the subpatchers open. The state of which windows are open (and which are not) is saved when you save the patch. It also saves the location of the windows on your screen.